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NAME

       visir_img_reduce  -  Combines a stack of chopped, jittered and/or nodded exposures and can
       compute the sensitivity for standard star observations

SYNOPSIS

       esorex visir_img_reduce [OPTIONS] FILE.sof

DESCRIPTION

       This recipe recombines the data observed in chopping/nodding or chopping or nodding  modes
       into one combined image using optionally cross-correlation methods.

       The    files    listed    in    the   Set   Of   Frames   (sof-file)   must   be   tagged:
       VISIR-observation-file.fits     IM_OBS_CHO_NOD_JIT     or      VISIR-observation-file.fits
       IM_OBS_CHO_JIT        or        VISIR-observation-file.fits        IM_OBS_NOD_JIT       or
       VISIR-observation-file.fits   IM_OBS_DIR_JIT    or    VISIR-observation-file.fits    BURST
       VISIR-Standard-star-catalog     IMG_STD_CATALOG    (optional)    VISIR-linearty-table.fits
       LINEARITY_TABLE (optional) Additionally, a bad pixel map with a PRO.CATG of IMG_BPM may be
       added to the Set Of Frames with tag: BPM.

OPTIONS

       --planestart <int>
              Plane  number to start repacking from in each nod cycle,earlier planes are skipped.
              (int; default: 0). The full name of this option for the EsoRex  configuration  file
              is visir.visir_util_repack.planestart [default = 0].

       --planelimit <int>
              Limit number of processed inputplanes. It will repack until at least this number of
              input images have been processed or the full dataset has been repacked. Always full
              chop  cycles  need  to  be  repacked  so  the number is adjusted upward to the next
              multiple of images per chop cycle.  <= 0 for no limit. (int; default: -1). The full
              name    of    this    option    for    the    EsoRex    configuration    file    is
              visir.visir_util_repack.planelimit [default = -1].

       --trimlow <int>
              Burst data only. Number of additional planes to cut from  before  each  plane  with
              chopper  movement.  (int;  default: 0). The full name of this option for the EsoRex
              configuration file is visir.visir_util_repack.trimlow [default = 0].

       --trimhigh <int>
              Burst data only. Number of additional planes to cut  from  after  each  plane  with
              chopper  movement.   A  value  of -1 does not skip the plane of the movement. (int;
              default: 0). The full name of this option for  the  EsoRex  configuration  file  is
              visir.visir_util_repack.trimhigh [default = 0].

       --lincorrect <bool>
              Apply  linearity  correction. Should only be enabled on high flux observations, may
              degrade results otherwise. (bool; default: False). The full name of this option for
              the  EsoRex  configuration  file  is  visir.visir_util_repack.lincorrect [default =
              False].

       --template <str>
              Correlation template used to detect shifts and reject bad images.  If none given an
              averaged image is used (str; default: ´NONE´). The full name of this option for the
              EsoRex configuration  file  is  visir.visir_util_detect_shift.template  [default  =
              NONE].

       --min-correlation <float>
              Minimal  correlation to the template required to be accepted (float; default: 0.5).
              The  full  name  of  this   option   for   the   EsoRex   configuration   file   is
              visir.visir_util_detect_shift.min-correlation [default = 0.5].

       --max-shift <float>
              Maximal  allowed  object  shift for an image to be accepted (float; default: 10.0).
              The  full  name  of  this   option   for   the   EsoRex   configuration   file   is
              visir.visir_util_detect_shift.max-shift [default = 10.0].

       --max-mad <float>
              Maximal allowed median absolute deviation for an image to be accepted.  <= 0 equals
              no limit (float; default: 0.0). The  full  name  of  this  option  for  the  EsoRex
              configuration file is visir.visir_util_detect_shift.max-mad [default = 0.0].

       --naverage <int>
              Number of planes to average before attempting to detect the shifts.  (int; default:
              1).  The  full  name  of  this  option  for  the  EsoRex  configuration   file   is
              visir.visir_util_detect_shift.naverage [default = 1].

       --method <str>
              Method  to  determine  beam  shifts.   xcorrelate: use the cross correlation shift.
              brightest: use the position of the brightest pixel  (str;  default:  ´xcorrelate´).
              The   full   name   of   this   option   for   the  EsoRex  configuration  file  is
              visir.visir_util_detect_shift.method [default = xcorrelate].

       --no-shift <bool>
              Sets whether to apply the determined shifts in following recipes. Set  to  TRUE  of
              shifts  appear  too large. (bool; default: False). The full name of this option for
              the EsoRex configuration file is visir.visir_util_detect_shift.no-shift [default  =
              False].

       --no-reject <bool>
              If  true images with bad statistics will not be rejected and no shift correction is
              done  (bool;  default:  True).  The  full  name  of  this  option  for  the  EsoRex
              configuration file is visir.visir_util_detect_shift.no-reject [default = True].

       --beampos <str>
              Define the positions of the beams. These positions are cut by the window to extract
              the single beam images.  Format: sign:x,y,window;sign:x,y,window;...    where  sign
              is  "pos"  or  "neg"  depending  on  whether the beam is positive or negative.  The
              window is optional and defines the size of the  cut  image  around  the  beam.  The
              default  window  is  the  chop  throw.   E.g.:  pos:50,60;neg:50,160;   By  default
              autodetection is attempted.  (str; default: ´NONE´). The full name of  this  option
              for the EsoRex configuration file is visir.visir_util_detect_shift.beampos [default
              = NONE].

       --eccmax <float>
              The maximum eccentricity allowed in the  combination  of  the  three  (in  parallel
              nod/chopping)  or  four  (in  perpendicular nod/chopping) beams.  In parallel mode,
              three perfectly aligned points spaced with the chopnod throw will have eccentricity
              0,  while  in  perpedicular mode a square with the chopnod throw as the side length
              will have eccentricity 0 (float; default: 3.0). The full name of  this  option  for
              the  EsoRex  configuration  file is visir.visir_util_detect_shift.eccmax [default =
              3.0].

       --keepfrac <float>
              The fraction of pixels to keep for the initialmedian  (float;  default:  0.9).  The
              full    name    of   this   option   for   the   EsoRex   configuration   file   is
              visir.visir_util_clip.keepfrac [default = 0.9].

       --kappa <float>
              Clip outside + or - kappa * sigma (the standard deviation) (float;  default:  5.0).
              The   full   name   of   this   option   for   the  EsoRex  configuration  file  is
              visir.visir_util_clip.kappa [default = 5.0].

       --maxite <int>
              Max number of kappa-sigma clipping iterations (int; default: 3). The full  name  of
              this  option  for  the  EsoRex  configuration  file is visir.visir_util_clip.maxite
              [default = 3].

       --shift-beams <bool>
              Account for movements of the object defined in CRPIX[12] (bool; default: True). The
              full    name    of   this   option   for   the   EsoRex   configuration   file   is
              visir.visir_util_clip.shift-beams [default = True].

       --error-source <str>
              Defines the way errors are generated:  img-stdev: stdev of image timeseries:  stdev
              of  each  pixel  over  the  time  axis of the cube  none: no error generation (str;
              default: ´img-stdev´). The full name of this option for  the  EsoRex  configuration
              file is visir.visir_util_clip.error-source [default = img-stdev].

       --badimage <float>
              If  percentage of clipped pixels above this value the whole image is considered bad
              (float; default: 0.2). The full name of this option for  the  EsoRex  configuration
              file is visir.visir_util_clip.badimage [default = 0.2].

       --output-all <bool>
              Output  a coadded image for each input file in addition to the complete coaddition.
              (bool; default: False). The full name of this option for the  EsoRex  configuration
              file is visir.visir_util_run_swarp.output-all [default = False].

       --extra_config <str>
              Additional  configuration  parameters (str; default: ´NONE´). The full name of this
              option for the EsoRex configuration file is visir.visir_util_run_swarp.extra_config
              [default = NONE].

       --config_fname <str>
              Swarp      configure     file     name.     (str;     default:     ´/usr/share/cpl-
              plugins/visir-4.3.7/config/visir_default.swarp´). The full name of this option  for
              the EsoRex configuration file is visir.visir_util_run_swarp.config_fname [default =
              /usr/share/cpl-plugins/visir-4.3.7/config/visir_default.swarp].

       --nprocs <int>
              Maximum number of swarp  processes  that  can  be  spawned  simultaneously.   (int;
              default:  -1).  The  full  name of this option for the EsoRex configuration file is
              visir.visir_util_run_swarp.nprocs [default = -1].

       --jy_val <float>
              The flux of the standard star in Jansky (float; default: -999.0). The full name  of
              this  option  for  the EsoRex configuration file is visir.visir_old_img_phot.jy_val
              [default = -999.0].

       --radii <str>
              Radii : star_max bg_int bg_ext (str; default: ´20-20-30´). The full  name  of  this
              option for the EsoRex configuration file is visir.visir_old_img_phot.radii [default
              = 20-20-30].

       --delete-temp <bool>
              Delete temporary files created during processing (bool; default:  True).  The  full
              name    of    this    option    for    the    EsoRex    configuration    file    is
              visir.visir_img_reduce.delete-temp [default = True].

       Note that it is possible to create a configuration file containing  these  options,  along
       with  suitable default values. Please refer to the details provided by the 'esorex --help'
       command.

SEE ALSO

       The full documentation for the visir pipeline can be downloaded as a PDF  file  using  the
       following URL:

              ftp://ftp.eso.org/pub/dfs/pipelines/visir/visir-pipeline-manual-1.4.pdf

       An   overview   over   the   existing   ESO  pipelines  can  be  found  on  the  web  page
       https://www.eso.org/sci/software/pipelines/.

       Basic documentation about the EsoRex program can be found at the esorex (1) man page.

       It is possible to call the pipelines  from  python  using  the  python-cpl  package.   See
       https://packages.python.org/python-cpl/index.html for further information.

       The   other   recipes  of  the  visir  pipeline  are  visir_img_dark(7),  visir_img_ff(7),
       visir_img_trans(7), visir_old_img_combine(7), visir_old_img_phot(7), visir_old_spc_obs(7),
       visir_old_spc_obs_ech(7),         visir_old_spc_phot(7),        visir_old_spc_phot_ech(7),
       visir_old_spc_wcal(7),       visir_old_spc_wcal_ech(7),        visir_old_util_destripe(7),
       visir_spc_reduce(7),             visir_util_apply_calib(7),            visir_util_clip(7),
       visir_util_convert_weight(7),    visir_util_detect_shift(7),    visir_util_img_std_cat(7),
       visir_util_join(7),   visir_util_qc(7),   visir_util_repack(7),   visir_util_run_swarp(7),
       visir_util_spc_std_cat(7), visir_util_spc_txt2fits(7), visir_util_undistort(7)

VERSION

       visir_img_reduce 4.3.7

AUTHOR

       Julian Taylor <jtaylor@partner.eso.org>

BUG REPORTS

       Please report any problems to  jtaylor@partner.eso.org.  Alternatively,  you  may  send  a
       report to the ESO User Support Department <usd-help@eso.org>.

LICENSE

       This  file  is  part of the VISIR Instrument Pipeline Copyright (C) 2015 European Southern
       Observatory

       This program is free software; you can redistribute it and/or modify it under the terms of
       the  GNU  General  Public  License  as  published  by the Free Software Foundation; either
       version 2 of the License, or (at your option) any later version.

       This program is distributed in the hope that it will be useful, but WITHOUT ANY  WARRANTY;
       without  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
       See the GNU General Public License for more details.

       You should have received a copy of the GNU General Public License along with this program;
       if  not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston,
       MA  02111-1307  USA